https://github.com/drpatelh/nf-core-sgrnaquant
UNDER CONSTRUCTION: CRISPR sgRNA quantification pipeline
https://github.com/drpatelh/nf-core-sgrnaquant
counting crispr crispr-analysis nextflow nf-core pipeline quantification sgrna workflow
Last synced: 3 months ago
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UNDER CONSTRUCTION: CRISPR sgRNA quantification pipeline
- Host: GitHub
- URL: https://github.com/drpatelh/nf-core-sgrnaquant
- Owner: drpatelh
- License: mit
- Created: 2019-09-27T12:28:53.000Z (over 5 years ago)
- Default Branch: master
- Last Pushed: 2019-09-27T16:32:35.000Z (over 5 years ago)
- Last Synced: 2025-01-13T12:46:36.579Z (4 months ago)
- Topics: counting, crispr, crispr-analysis, nextflow, nf-core, pipeline, quantification, sgrna, workflow
- Language: Nextflow
- Homepage: http://nf-co.re
- Size: 64.5 KB
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- Changelog: CHANGELOG.md
- Contributing: .github/CONTRIBUTING.md
- License: LICENSE
- Code of conduct: CODE_OF_CONDUCT.md
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README
# 
[](https://travis-ci.com/nf-core/sgrnaquant)
[](https://www.nextflow.io/)
[](http://bioconda.github.io/)
[](https://hub.docker.com/r/nfcore/sgrnaquant)
## Introduction
**nfcore/sgrnaquant** is a bioinformatics analysis pipeline used for the quantification of CRISPR sgRNA guides obtained from Illumina sequencing.
The pipeline is built using [Nextflow](https://www.nextflow.io), a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It comes with docker containers making installation trivial and results highly reproducible.
## Pipeline summary
1. Raw read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))
2. Adapter trimming ([`cutadapt`](https://cutadapt.readthedocs.io/en/stable/guide.html))
3. Alignment ([`BWA`](https://sourceforge.net/projects/bio-bwa/files/))
4. Count reads and split by strand after filtering ([`Pysam`](http://pysam.readthedocs.io/en/latest/installation.html) to remove:
1. reads that are unmapped
2. reads that map to multiple guides
3. reads containing > 0 mismatches
5. Present QC for raw read, alignment and filtering results ([`MultiQC`](http://multiqc.info/))
## Quick Start
i. Install [`nextflow`](https://nf-co.re/usage/installation)
ii. Install one of [`docker`](https://docs.docker.com/engine/installation/), [`singularity`](https://www.sylabs.io/guides/3.0/user-guide/) or [`conda`](https://conda.io/miniconda.html)
iii. Download the pipeline and test it on a minimal dataset with a single command
```bash
nextflow run nf-core/sgrnaquant -profile test,
```
iv. Start running your own analysis!
```bash
nextflow run nf-core/sgrnaquant -profile --design design.csv
```
See [usage docs](docs/usage.md) for all of the available options when running the pipeline.
## Documentation
The nf-core/sgrnaquant pipeline comes with documentation about the pipeline, found in the `docs/` directory:
1. [Installation](https://nf-co.re/usage/installation)
2. Pipeline configuration
* [Local installation](https://nf-co.re/usage/local_installation)
* [Adding your own system config](https://nf-co.re/usage/adding_own_config)
3. [Running the pipeline](docs/usage.md)
4. [Output and how to interpret the results](docs/output.md)
5. [Troubleshooting](https://nf-co.re/usage/troubleshooting)
## Credits
The pipeline was originally written by [The Bioinformatics & Biostatistics Group](https://www.crick.ac.uk/research/science-technology-platforms/bioinformatics-and-biostatistics/) for use at [The Francis Crick Institute](https://www.crick.ac.uk/), London.
The pipeline was developed by [Harshil Patel](mailto:[email protected]).
## Citation
You can cite the `nf-core` pre-print as follows:
Ewels PA, Peltzer A, Fillinger S, Alneberg JA, Patel H, Wilm A, Garcia MU, Di Tommaso P, Nahnsen S. **nf-core: Community curated bioinformatics pipelines**. *bioRxiv*. 2019. p. 610741. [doi: 10.1101/610741](https://www.biorxiv.org/content/10.1101/610741v1).